bioenergetics unit 1

8/12/2019 Bioenergetics Unit 1

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2 Cell &iology



Unit 1: Bioenergetics:

CONTENTS

'ntroduction

Learning (b)ecti%es

*.*

Summary

+eywords

-ercise

$urther eadings

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!abulated standard9state thermodynamic data are generally for a temperature of ; C 4 <= +6

St nd rd St te ree Energ' o& or* tion - & /

!he change in free energy that occurs when a compound is formed from its elements in their most thermodynamically stablestates at standard9state conditions. 'n other words, it is the difference between the free energy of a substance and the freeenergies of its elements in their most thermodynamically stable states at standard9state conditions.

!he standard9state free energy of reaction can be calculated from the standard9state free energies of formation as well. 't isthe sum of the free energies of formation of the products minus the sum of the free energies of formation of the reactants:

S#(>!A> (US: is negati%e 4 ? 8, + e1 @ *6

>(>9S#(>!A>(US: is positi%e 4 @ 8, + e1 ? *6

U'L'& 'UM: B 8 4+ e1 B *6

'f a reaction is fa%orable for both enthalpy 4 5 ? 8 6 and entropy 4 S @ 86 changes, then the reaction

will be S#(>!A> (US 4 ? 8 6 at any temperature.

'f a reaction is unfa%orable for both enthalpy 4 5 @ 8 6 and entropy 4 S ? 8 6 changes, then the reaction

will be >(>9S#(>!A> (US 4 @ 8 6 at any temperature.

'f a reaction is fa%orable for only one of either entropy or enthalpy, the standard9state free energy e1uationmust be used to determine whether the reaction is spontaneous or not.

$or non9standard9state conditions 4# 8.* M#aD concentrations * M6, %alues of 5 and S for the actualreaction conditions must be calculated and used to determine and + e1.

S *%+e &ree energ' c +cu+ tion -st nd rd st te conditions/:

Co*%ound . & S >5 E >( F4 s6 9FG;.;G *;*.8=

>5 EH4aq 6 9*F .;* **F.E >( F

94aq 6 9 8;.8 *EG.E

C +cu+ te . 5 S 5 nd &or t(e !o#e re ction to deter*ine )(et(er t(e re ctionis s%ont neous or not$

$irst letIs calculate . & . >ote that in the abo%e reaction, one mole of >5 E >( F dissociates in water togi%e one mole each of >5 E

H and >( F9:

>e-t, letIs calculate S :

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>ow we can plug in these %alues weI%e calculated into the free energy e1uation.

7 NOTE: !he units of . & is ,7 and the units of S is 780 . Since is generally reported in,7 , we can di%ide S by *888 to con%ert it to units of ,780 7 NOTE: !he temperature in the free energy e1uation must be in +el%in, so we must con%ert the gi%entemperature in Celsius to +el%in by adding JF.*;.

C(ec, Your 9rogress 1

Mu+ti%+e C(oice uestion:

Cell is disco%ered by:

a6 obert 5ook

b6 Kakob Schleiden

c6 !heodor Schwann

d6 udolf irchow

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; Cell &iology



*. Deter*in tion o& &or re ction Re+ tions(i% !et)een St nd rd reeenerg' c( nge nd E<ui+i!riu* Const nts

!he following e1uation relates the standard9state free energy of reaction with the free energy of reaction at any moment intime during a reaction 4not necessarily at standard9state conditions6:

7 B free energy at any moment

7 B standard9state free energy

7 B ideal gas constant B =.F*E K"mol9+

7 ! B temperature 4+el%in67 ln B natural log of the re ction <uotient

Re ction <uotient - c or %/ 9 !he mathematical product of the concentrations 4or partial pressures6 of the products of a reaction di%ided by the mathematical product of the concentrations 4or partial pressures6 reactants of a reactionA! A> M(M >! '> !'M .

Note: Nhen c B + c 4or when p B + p6, a reaction is at e1uilibrium.

't was stated earlier that when B 8, a reaction is at e1uilibrium. LetIs consider the abo%e reaction at e1uilibrium:

'f we mo%e !ln+ to the opposite side by subtracting it from both sides, we get the following reaction which relates the freeenergy of a reaction to the e1uilibrium constant of a reaction:

S9ONT=NEOUS NON S9ONT=NEOUS

? 8 + @ *

@ 8 + ? *

!he magnitude of measures how far a reaction is from e1uilibrium. !he larger the %alue of , the further thereaction is from e1uilibrium and the further the reaction must shift to reach e1uilibrium. 'n reactions in which enthalpy is

fa%orable and entropy is unfa%orable, the reaction becomes less spontaneous 4 increases6 until e%entually the reaction is

not spontaneous 4when @ 86. As the magnitude of changes, so does the e1uilibrium constant. +.

!he &ree energ' c( nge - / of a reaction determines its spontaneity. !he free energy change 4 ∆ 6, and its relation toe1uilibrium constant. A reaction is s%ont neous i& is neg ti#e 4if the free energy of the products is less than the freeenergy of the reactants6.

B change in free energy, o> B standard free energy change 4with * M reactants and products, at p5 J6,R B gas constant, T B absolute temperature.

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>ote that the standard free energy change 4 ∆ oI6 of a reaction may be positi%e, for e-ample, and the actual free energy change4∆ 6 negati%e, depending on cellular concentrations of reactants and products. Many reactions for which ∆ oI is positi%e arespontaneous because other reactions cause depletion of products or maintenance of high substrate concentrations.

At e<ui+i!riu* , e1uals 3ero. Sol%ing for o>yields the relationship at left.

0> e<, the ratio OCPO/P"OAPO&P at e1uilibrium, is called thee<ui+i!riu* const nt .

=n e<ui+i!riu* const nt gre ter t( n one 4more products than reactants ate1uilibrium6 indicates a s%ont neous re ction 4negati%e ∆ I6.

!he %ariation of e1uilibrium constant with ∆ oI is shown in the table below.

0 e< o> 4kK"mol6 Starting with * M reactants and products, the reaction:

1@4 A 23 proceeds forward 4spontaneous6

1@2 A 11 proceeds forward 4spontaneous6

1@@ 1 @ is at e<ui+i!riu*

1@ A2 11 proceeds in re%erse

1@ A4 23 proceeds in re%erse

Energ' cou%+ing

A spontaneous reaction may dri%e a non9spontaneous reaction.

Bio+ogic + st nd rd st te St nd rd ree Energ' C( nge in Cou%+edre ctions$

Cou%+ed Re ctions

!wo reactions are said to be coupled when the product of one of them is the reactant in the other:

AQ & &Q C

'f the standard free energy of the first reaction is positi%e but that of the second reaction is sufficientlynegati%e, then for the o%erall process will be negati%e and we say that the first reaction is Rdri%en by the

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Cell &iology



second one. !his, of course, is )ust another way of describing an effect that you already know as the LeChTtelier principle: the remo%al of substance & by the second reaction causes the e1uilibrium of the firstto Rshift to the right . Similarly, the e1uilibrium constant of the o%erall reaction is the product of the

e1uilibrium constants of the two steps.

1 Cu S4s6 Q Cu4s6 H S4s6 GV B H =G. kK H V B H JG.F kK

2 S4s6 H ( 4g6Q S( 4g6 GV B WF88.* kK H V B H <G.= kK

3 Cu S4s6Q Cu4s6 H S( 4g6 GV B W *F.< kK H V B W *J.F kK

'n the abo%e e-ample, reaction 1 is the first step in obtaining metalliccopper from one of its principal ores. !his reaction is endothermic and ithas a positi%e free energy change, so it will not proceed spontaneously atany temperature. 'f Cu S is heated in the air, howe%er, the sulfur is

remo%ed as rapidly as it is formed by o-idation in the highly spontaneousreaction 2, which supplies the free energy re1uired to dri%e 1. !hecombined process, known as ro sting , is of considerable industrialimportance and is one of a large class of processes employed for winningmetals from their ores .

ree energ' c( nges of coupled reactions are dditi#e .

-amples of different types of coupling:

=$ Some en3yme9cataly3ed reactions are interpretable as t)o cou%+ed ( +& re ctions , one spontaneous and the other non9spontaneous. At the en3yme acti%e site, the coupled reaction is kinetically facilitated, while the indi%idual half9reactions are

pre%ented. !he free energy changes of the half9reactions may be summed, to yield the free energy of the coupled reaction.

$or e-ample, in the reaction cataly3ed by the lycolysis en3yme 5e-okinase , the two half9reactions are:

A!# H 5 ( A/# H # i .................. ∆ oI B− F* kKoules"mol

# i H glucose glucose9G9# H 5 ( ... ∆ oI B H*E kKoules"mol

Cou%+ed re ction: A!# H glucose A/# H glucose9G9# .. ∆ oI B − *J kKoules"mol!he structure of the en3yme acti%e site, from which water is e-cluded, pre%ents the indi%idual hydrolytic reactions, whilefa%oring the coupled reaction.

B$ !wo separate en3yme9cataly3ed reactions occurring in the same cellular compartment, one spontaneous and the other non9spontaneous, may be coupled by a co**on inter*edi te 4reactant or product6.

9'ro%(os%( te 4## i6 is often the product of a reaction that needs a dri%ing force. 'ts spontaneous hydrolysis, cataly3ed by#yrophosphatase en3yme, dri%es the reaction for which ## i is a product. $or an e-ample of such a reaction, see the discussionof cAM# formation below.

C . Ion tr ns%ort may be cou%+ed to c(e*ic + re ction , e.g., hydrolysis orsynthesis of A!#.

'n the diagram at right and below, water is not shown. 't should be recalled that theA!# hydrolysis"synthesis reaction is A!# H 5 ( A/# H # i.

1ui%alent to e1uation, the free energy change 4electrochemical potential difference6

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https://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/glycolysis.htm#Hexokinase

https://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/bioener.htm#camp



https://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/glycolysis.htm#Hexokinase




associated with transport of an ion S across a membrane from side * to side isrepresented below.

R B gas constant, T temperature, G B chargeon the ion, B $araday constant, and B%oltage across the membrane.

Since free energy changes are additi%e, the s%ont neous direction for the coupled reaction will depend on the re+ ti#e* gnitudes of:

&or t(e ion &+uH 4∆ %aries with the ion gradient and %oltage.6

&or t(e c(e*ic + re ction 4∆ oI is negati%e in the direction of A!# hydrolysis. !he magnitude of ∆ depends also onconcentrations of A!#, A/#, and # i .6

!wo e-amples of such coupling are:

*. =cti#e tr ns%ort$ Spontaneous A!# hydrolysis 4negati%e ∆ 6 is coupled to4dri%es6 ion flu- against a gradient 4positi%e ∆ 6. $or an e-ample, see the discussionof S CA .

. =T9 s'nt(esis in mitochondria. Spontaneous 5 H flu- across a membrane 4negati%e∆ 6 is coupled to 4dri%es6 A!# synthesis 4positi%e ∆ 6. See the discussion of the A!#Synthase .

Kust as commerce is facilitated by the use of a common currency, the commerce of the cellXmetabolism Xis facilitated by the use of a common energy currency, adenosine triphosphate 4A!# 6. #art of the freeenergy deri%ed from the o-idation of foodstuffs and from light is transformed into this highly accessiblemolecule, which acts as the free9energy donor in most energy9re1uiring processes such as motion, acti%etransport, or biosynthesis.

A!# is a nucleotide consisting of an adenine, a ribose, and a triphosphate . !he acti%e form of A!# isusually a comple- of A!# with Mg H or Mn H . 'n considering the role of A!# as an energy carrier, wecan focus on its triphosphate moiety. ATP is an energy-rich molecule because its triphosphate unit

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1@ Cell &iology

https://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/carriers.htm#P-class

https://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/f1fo.htm



http://www.ncbi.nlm.nih.gov/books/n/stryer/A5607/def-item/A5617/


https://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/carriers.htm#P-class







contains two phosphoanhydride bonds . A large amount of free energy is liberated when A!# ishydroly3ed to adenosine diphosphate 4 A/# 6 and orthophosphate 4 # i6 or when A!# is hydroly3ed toadenosine monophosphate 4 AM# 6 and pyrophosphate 4 ## i6.

Structures of A!#, A/#, and AM#. !hese adenylates consist of adenine 4blue6, a ribose 4black6, and atri9, di9, or monophosphate unit 4red6. !he innermost phosphorus atom of A!# is designated # Y, themiddle one # Z, and the outermost one

!he precise GV[ for these reactions depends on the ionic strength of the medium and on theconcentrations of Mg H and other metal ions. Under typical cellular concentrations, the actual G forthese hydrolyses is appro-imately 9* kcal mol 9* 49;8 kK mol9*6.

!he free energy liberated in the hydrolysis of A!# is harnessed to dri%e reactions that re1uire an input offree energy, such as muscle contraction. 'n turn, A!# is formed from A/# and # i when fuel moleculesare o-idi3ed in chemotrophs or when light is trapped by phototrophs. This ATP—ADP cycle is the

fundamental mode of energy exchange in biological systems

Some biosynthetic reactions are dri%en by hydrolysis of nucleoside triphosphates that are analogous toA!# Xnamely, guanosine triphosphate 4 !# 6, uridine triphosphate 4 U!# 6, and cytidine triphosphate4C!# 6. !he diphosphate forms of these nucleotides are denoted by /# , U/# , and C/# , and themonophosphate forms by M# , UM# , and CM# . n3ymes can cataly3e the transfer of the terminal

phosphoryl group from one nucleotide to another. !he phosphorylation of nucleoside monophosphates iscataly3ed by a family of nucleoside monophosphate kinases, as discussed in Section <.E.* . !he

phosphorylation of nucleoside diphosphates is cataly3ed by nucleoside diphosphate kinase, an en3ymewith broad specificity. 't is intriguing to note that, although all of the nucleotide triphosphates areenergetically e1ui%alent, A!# is nonetheless the primary cellular energy carrier. 'n addition, twoimportant electron carriers, >A/ H and $A/ , are deri%ati%es of A!#. The role of ATP in energymetabolism is paramount .

C(ec, Your 9rogress 2

Mu+ti%+e C(oice uestions

T(e ter*s %ro, r'otic nd eu, r'otic )ere suggested !'

a6 5ans is

b6 Kakob Schleiden

c6 !heodor Schwann

d6 obert 5ook

Cell &iology 11

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http://www.ncbi.nlm.nih.gov/books/n/stryer/A1236/#A1238






























Le rner =cti#it'

Analyse the +ey functions of all cell organelles.

Su** r'

0e')ords

EHercise

=ns)ers to C(ec, Your 9rogress uestions

CYP 1

obert 5ook

CYP 2

5ans isCYP 3

*. * \m to *8 \m. ram9negati%eF. #lasmidsE. &acterial

Cyp 4

a6 !rue

b6 $alse

c6 !rue

d6 $alse CYP 2

*.

urt(er Re dings

e! Lin,s

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12 Cell &iology

bioenergetics unit 1

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